I do it to help key in the top and as insurance for those who like to tap (pound) on the top.

If the brace is not inletted, and somebody knocks the top over the brace with a microphone, say (I know YOU would not do that, but it happens...) the top will bend and the brace will not. This puts a lot of peeling stress on the glue line, and glue is not good at that, so the brace will tend to peel loose.

Back when I did more repairs I used to get in old Gibsons with loose or missing upper transverse braces. They used to scoop out the very end of the braces over a short distance with a sander, just about down to nothing. Rather than cutting pockets for the brace ends, they seem to have simply mashed everything down with clamps, counting on the brace end to compress the liner the small amount that was needed. Since both the bracing and the liner were spruce is happens every so often that the liner will be harder than the brace wood, and it's the brace end that gets crushed. This essentially severs the brace end just inside the liner, and eventually, with the download on it, it peels loose. In a couple of cases the player found the stick rattling around inside the box, and tossed it out. Then the action got really high....

Two brads will locate it instantly. I place one brad in the neck block under the fingerboard, and one on the outer edge of the tail block, where the binding and purfling grooves will be routed. The brads are removed after the glue sets.

With the brads, it makes no difference what the orientation of the body is. Gluing top down is better, since it eliminates having excess glue run down the sides. I apply the glue with the sides turned top side up....I like to install the top before flipping the body over and clamping it. The brads hold the top in the proper alignment during the flipping and clamping, which is why I use them.

As you say, the holes for the brads are drilled pre-glueup when the top is properly aligned. The brads are inserted in the top, and remain there until the gluing is done. In other words, the brads are already in the top when it goes on the rim.

I use the same type of brads when gluing bridges, fingerboards, and peghead veneers. They are 1/2" long and 17 AWG (0.045" dia). I use a #56 drill bit. Sometimes I cut them shorter, particularly for the thinner peghead veneers.

These brads have a small head on them, so they are inserted from the outside. The head remains above the surface after the gluing, which helps when removing them.